While I agree that crafting gets way out of control once you have a high level of skill in more than one of the three methods, at the same time the fact you can make really powerful stuff keeps those skills relevant compared to the unique items that can only be found/earned. After all, if you can find better stuff than you can ever make, then nobody's going to bother with crafting unless their RP requires it.
That said, if you compare said unique items to crafted ones made using only one of the three skills, you'll find that the former are often significantly better due to the (sometimes rather heavy) diminishing returns built into the crafting formulas. This is especially true for Enchanting, which by itself cannot match the enchantments on some of the standard items, let alone the unique ones. Which begs the question of exactly what sort of crafted items the unique ones should be compared to, since the power level of the latter is deliberately clamped in order to keep from breaking the game once you get one.
There's also the question of just how difficult it should be to get a unique item, which is a long-standing conundrum. One way to do it is to require another item of a similar power level; while this makes sense given their power, doing so can render both unobtainable since you can't get one without the other. Another way is to allow it to be obtained without using another such item; the problem here is that doing so can render them both irrelevant since you're already strong enough without them.
Here's another important question: just how special should a unique item be? I'm pretty sure that nobody here wants them to reach the same level of efficacy triple-stacked crafted items can, however the existence of this thread indicates that they're clearly not special enough in their current form(s).
You don't need more than one maxed out craft, namely blacksmithing, to blow the shorts off of every unique in the game. And it doesn't even have to be maxed, and you only need to have two or three moderate +smithing items you bought from a vendor, and a +50 smithing potion- a number of which I've looted or stolen just laying around in the gameworld. You don't even need to have done ANY enchanting or alchemy, at all. Armed just with those things, you can improve easily-made ebony and daedric weapons (and any armors you care to mess with) to be markedly superior to all unique weapons and armor. Of course, you can use these same methods to improve a number of the uniques to be almost as good, but none will be any better.
Unique items should be better than anything you can craft, period. What is the point in having them in the game, if they're not? They just turn into wall decorations or get put on the mantlepiece, because they are inferior to easily-crafted stuff. This trivializes them to the point of wondering why they even bothered adding them in, to be honest. Crafting should never be more than a means to *moderately* improve items, whether they be normal items, created items, uniques, or whatever. They should have made it so that no combination of crafting techniques could improve any item more than maybe 25 or 50% above it's base level, and unique items should start out at maybe 20% better than the best equivalent normal item in the game.
So, instead of crafting normal ebony or daedric weapons that can very easily be improved to be 200%, 500%, or thousands of % better if you want to get whacky (but still well within the 'normal' capabilities built into the game, mind you), you would have reasonably improved weapons that would do quite well for most situations, until or unless you discovered one of the notably better uniques... which could also be improved moderately to maintain their proper damage lead over the pure crafted gear that's been upgraded. So, by doing this, you get rid of the crazy-stupid overpowered craft gear, you make uniques valuable and desireable again, as they should be... and you make game balance MUCH easier, since you maintain a logical and intelligent damage range un-F'ed-up by the current crafting mess.
Crafting, in any game, is secondary. It is a mini-game for occasional distraction from the usual dungeon diving and questing and whathaveyou. It was not intended, and should never be intended, to overshadow all other methods of item acquisition in a game, especially not to the point where it makes bothering to look for non-crafted gear a moot point and a waste of effort, and entirely removes any interest from the looting aspect.